Ash O'Farrell

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3. basename() does not function as expected on DRS URIs

Thanks for always being quick to respond Jason! It's much appreciated!

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• August 19, 2021 16:07
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3. Is it possible to have a task directly modify an input file?

I might be barking up the wrong tree here, but it seems that when Terra localizes files, those files are considered owned by root instead of the topmed user (which is considered the owner on local ...

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• August 11, 2021 21:30
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3. Is it possible to have a task directly modify an input file?

Interestingly, when I run this modified workflow on Terra, whoami still resolves to the topmed user, and the topmed user still is in the sudo group. Who am I? topmed What's in the group database? r...

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• August 11, 2021 21:10
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3. Is it possible to have a task directly modify an input file?

I made some edits to my workflow to print this information: https://dockstore.org/workflows/github.com/DataBiosphere/analysis_pipeline_WDL/vcf-to-gds-wdl:debug-permissions?tab=files Two quick notes...

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• August 11, 2021 21:05
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3. Is it possible to have a task directly modify an input file?

Thank you for your response and testing, it's helpful to know this has something to do with the container permissions. However, it seems to raise even more questions. When I run the WDL locally via...

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• August 05, 2021 18:58
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3. Cannot update workflow if current snapshot active on Terra becomes invalid

The workaround you listed is functional, thank you!

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• May 25, 2021 00:31
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3. Terra seems to have destroyed my output

That's interesting. Thanks for the explanation! Does Terra's version of Cromwell match the current release schedule as Cromwell on Github, or is it on its own release schedule?

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• May 12, 2021 17:49
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3. Terra seems to have destroyed my output

The underlying cause makes sense, but ultimately I'm still confused why Terra reported the workflow a success. Normally, when Cromwell cannot find an output (lets say my output file is merged.gds b...

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• May 12, 2021 17:27
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3. Terra seems to have destroyed my output

It turns out I need to get a working version of this pipeline out sooner than anticipated, so I have to implement a workaround. My colleague Julian came up with one that uses globbing. The workarou...

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• May 10, 2021 19:07
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3. Terra seems to have destroyed my output

Thanks for letting me know. I'll hold off on the rewrite for now; any insight they provide would be worth its weight in gold if it helps me write better workflows in the future. I am generating the...

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• May 07, 2021 18:42
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